The Eleventh Doctor was once imprisoned in the Tower without trial on the personal order of King Charles II. Two days later, a sphere twenty feet across was seen heading away from the tower carrying the Doctor. (TV: The Impossible Astronaut)

In the early morning of 1 January2005, the newly regenerated Eleventh Doctor flew west over the Tower, whilst clinging by his fingers from his TARDIS' doorway, before climbing back aboard and being thrown nearly nine years back in time. (TV: The Eleventh Hour)

When the Department controlled Britain around the year 2050, the Tower of London became Dauntless Prison, a prison for all the aliens that arrived on Earth. When K9 Mark 2 and his friends released the alien prisoners there in 2050, the Department's treatment of the prisoners was leaked to the media and the prison was shut down. (TV: Liberation)

Some time around the 29th century onwards, during the reign of Elizabeth X, the tower or a new facility named after the original tower, was incorporated into Starship UK. Its dungeon contained the devices used to torture the star whale beneath the craft into moving. Amy Pond visited the Tower during this period with the Eleventh Doctor. (TV: The Beast Below)